maigesDE-class: maigesDE class, store results of differential gene expression...

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

Description

This class defines a structure to store the results from differential expression analysis. This type of analysis can be done using the functions deGenes2by2Ttest, deGenes2by2Wilcox and deGenes2by2BootT for analysis between two biological sample types, or function deGenesANOVA, for analysis between more than two sample types using ANOVA models.

Details

Objects of this class are produced by calling the functions deGenes2by2Ttest, deGenes2by2Wilcox and deGenes2by2BootT over an object of class maiges or by calling the function deGenesANOVA over an object of class maigesANOVA fitting an ANOVA model to the microarray dataset.

Slots

GeneInfo:

data frame containing the information regarding the genes from the dataset.

SampleInfo:

data frame similar to the GeneInfo above, but containing information about the biological sample types used in the analysis.

fold:

numerical matrix containing the fold values (mean difference between the sample types) when two sample types were compared. Each matrix column gives one specific test.

stat:

numerical matrix giving the statistic of the tests that were done. Each column represents on test.

p.value:

numerical matrix giving the p-values of the statistical tests. Again, each column represents different tests.

factors:

character string giving the biological factors used in ANOVA model (when ANOVA models were used).

test:

character string describing the test done.

Date:

character string giving date and time that the object were created.

V.info:

list containg three characters. The first one is a string containing the R version used when the object was created. The second is a char vector with base packages and the last one is another char vector with additional packages and version numbers.

Methods

plot

signature(x = 'maigesDE'): plot method for maigesDE class. Display volcano plots.

print

signature(x = 'maigesDE'): print method for maigesDE class.

show

signature(x = 'maigesDE'): show method for maigesDE class.

summary

signature(x = 'maigesDE'): summary method for maigesDE class.

Author(s)

Gustavo H. Esteves <[e-mail]>

See Also

deGenes2by2Ttest, deGenes2by2Wilcox, deGenes2by2BootT, deGenesANOVA.

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.